The Doctor and Rose are taken to Davros (Julian Bleach), creator of the Daleks. The Doctor taunts Davros on account of the fact he is not in charge (Davros having been imprisoned and kept alive for his knowledge), but Davros in turn retorts that the Doctor is as much a monster as he. Davros explains that the twenty-seven stolen planets form a compression field which can cancel the electrical energy of atoms. The resulting "reality bomb" has the potential to destroy all matter in every universe; reality itself would be destroyed. After the device is tested, the Daleks receive two transmissions: Sarah, Mickey, Jack, and Jackie threaten to destroy the Crucible using a "Warpstar" that Sarah Jane had, and Martha threatens to use the Osterhagen Key—a last resort device which would destroy Earth. Their actions cause Davros to challenge the Doctor's reliance on his companions. The companions, however, are transported to the Vault before they can execute their plans, where upon Davros gloats over his seeming victory and challenges the Doctor over the deaths he has caused and the sheer number of people who have died for him. Davros calls this my final victory; I have shown you yourself, Doctor.
Davros prepares to detonate the reality bomb before the TARDIS materialises in front of him. The second Doctor and Donna run out but are stopped by Davros. Seconds before the bomb detonates, Donna becomes imbued with Time Lord knowledge and disables the reality bomb. The two Doctors help her disable the Daleks and relocate the missing planets, but the control panel is destroyed by the Supreme Dalek before Earth can be relocated. Davros asks Dalek Caan why he didn't forsee this, but the Doctor realises he had. Caan confirms this, citing that having witnessed the atrocities committed by the Daleks throughout time and space, Caan sought to bring an end to it.
Motivated by Dalek Caan's prophecy of the Daleks' extinction, and knowing the Daleks could still take the Universe by force, with or without the Reality Bomb, the new Doctor destroys the Daleks and the Crucible. The original Doctor offers to save Davros who refuses, accusing the Doctor of being responsible for the destruction and naming him as "the Destroyer of Worlds". The companions flee into the TARDIS and "tow" the Earth back into its original orbit with the aid of Sarah's supercomputer Mr Smith, her robotic dog K-9, and the spatio-temporal rift in Cardiff.
In the dénouement of the episode, the Doctor parts ways with his companions: Sarah returns home to her son Luke; Martha and Mickey leave with Jack; and the Doctor returns Rose and Jackie to the parallel universe they were trapped in, in "Doomsday". The Doctor forces the other Doctor to stay in the parallel universe as punishment for committing genocide and to requite Rose's love. After departing, Donna becomes overwhelmed by the Time Lord knowledge. To save her life, the Doctor is forced to wipe her mind, and explains to her mother Sylvia (Jacqueline King) and grandfather Wilfred Mott (Bernard Cribbins) that Donna must never remember him, because she will die if she does so, even for a second. As the Doctor leaves, Wilfred promises that he will never forget the Doctor on his granddaughter's behalf.
The fictional Dårlig Ulv Stranden (Norwegian: Bad Wolf Bay) seen at the end of "Doomsday", is revisited. The Doctor's reply to Rose's statement of love is specified to Rose but left unheard; Davies deliberately left the reply ambiguous when he wrote "Doomsday". Executive producer Julie Gardner stated on the "Doomsday" commentary and the Doctor Who Confidential special for "Journey's End" that the Doctor requited her love.
In the BBC commentary for this episode, Phil Collinson and Julie Gardner describe a brief additional scene with Donna which was cut from the final episode:
"There was an additional Donna bit after this goodbye from the Doctor, which is when he goes outside into the TARDIS, we cut back into the kitchen, and there's a moment where Donna hears the TARDIS... there's a moment of realisation, and then she turns back round and carries on talking into the phone."
Gardner considered this scene untruthful and too confusing, since Donna remembering would lead to her death, and since she didn't recognise the Doctor it wouldn't make sense to assume she would recognise the noise of the TARDIS.
Blue Peter presenter Gethin Jones controlled one of the Daleks that escorts the human prisoners aboard the Crucible. He previously played a Cyberman in "Rise of the Cybermen" and has made a cameo appearance as himself in Doctor Who spin-off The Sarah Jane Adventures in the episode "Invasion of the Bane".
Harper is then shown directing a scene in which both Regan and Tennant are shown around the TARDIS console. Harper explains that in "two or three wide shots" they were able to use Regan and Tennant together. For the most part the double is used for scenes where one or the other Doctor is only seen from behind, or only an arm or back of the head is seen in a shot. The double has appeared in other episodes throughout the series. Over documentary footage showing the shooting of the scene where the new Doctor emerges from the TARDIS, Tennant describes the procedure for making an effects shot involving Tennant as both Doctors. The camera is locked in place while Tennant goes off and changes clothing, with Regan holding his place. A shot is made for reference with Regan, then another shot is made without Regan. This enables the shots to be merged during editing to create the effect of having David Tennant in two places in the same shot.
"Journey's End" was watched by 10.57 million viewers when broadcast on BBC1, giving it a 45.9% share of the total television audience. The episode was the most-viewed programme of the week; "Journey's End" is the first Doctor Who episode to receive this rank. It also received an Appreciation Index score of 91, equalling the record for the programme set by its predecessor "The Stolen Earth". A story on the BBC News website described fan reaction of the serials on the Digital Spy and Ain't It Cool News forums as "mixed".
Mark Wright of The Stage likens "Journey’s End" to "one big house of cards...[that] will come crashing down" if thought about too much. However, he had no problem with the resolution of "The Stolen Earth"'s cliffhanger and is critical of those who complain about feeling cheated by the lack of a regeneration. Though he expresses that he saw little need for Mickey and Jackie in this episode, he asserts that Donna had "the saddest end for a companion ever" and praises Davies for just managing to keep the plot together. He argues that as Davies "writes the emotions and big themes so well...blow logic and rational plot moments if they get in the way!" He compares Davies's writing style to "PT Barnum showmanship" and praises both the dark and light elements of the episode. He concludes that, if not overthought, the episode remains "an audacious, big, silly, often poignant season finale".
Writing for The Mirror, Jim Shelley is highly critical of this episode in his review describing it as "[d]emented rather than dazzling". He was confused by the two Doctors played by David Tennant, saw little development in Donna across the series and was puzzled by the Doctor's attempt to save his arch-enemy, Davros. He claims that "amidst all the shrieking, shouting, and mock operatic bluster, [he was] sure [he] saw a kitchen sink thrown in for good measure. Riddled with scientific mumbo-jumbo, it was too chaotic and long-winded to be the classic farewell Russell T Davies promised." He argues that the plot "went haywire" and that "Rose and the two Tennants acted out a sort of twisted menage a trois." In conclusion he states "Tennant's cheeky chappie mannerisms made the show into an extraterrestrial EastEnders."
In Scotland's Daily Record, Paul English called the episode "yet another fizzing Doctor Who adventure" and said that "Writer and producer Russell T Davies makes TV with the epic feel of the movies. He gets more tension, humour and emotion into an hour of telly than many films manage in twice the time with double the budget." He lamented that "Journey's End" "lacked the goofiness" of the series' 2005 return, but concluded that the finale was "TV gold".
Dave Golder of SFX says "If, while your brain is telling you, 'This is crap!' your heart is still doing backflips then it's your kind of episode. 'Journey's End' is almost a two fingers up at technobabble; there's certainly tons of it in the episode, but it's largely irrelevant." He praises the action sequences and the portrayal of Donna, Davros, Rose and the Doctor, but remarks that the overcrowding of minor characters made parts of the script seem "underdeveloped" and describes the Daleks as mostly "[c]annon fodder". "[The] plot does hang together, but only just". Overall, he describes the episode as "exceptional" but "not perfect".
Ben Rawson-Jones of Digital Spy describes the episode as "a satisfying and epic crowdpleasing conclusion" to the series and particularly praises Tate and Donna's exit. He states the episode mixes poignant and haunting scenes with "'punch the air' moments and fan-pleasing twists." Noting the episode is "not entirely flawless", he is critical of the Daleks' seemingly "too convenient" demise arguing that it undermines their menace. Writing for the Doctor Who blog on the Radio Times website, William Gallagher called "Journey's End" "event drama" and "party television". He stated that the resolution to the regeneration cliff-hanger left him feeling "a bit cheated", but praised the episode's characterisation, concluding that David Tennant "has been the best Doctor of them all" and that "Doctor Who is the best drama on TV: it's the one with most verve and spark and exuberant excitement. John Beresford of TV Scoop called the finale "just about the most exciting Doctor Who episode [he could] ever remember", and "a fantastically imaginative, exciting and action-packed finale to the fourth series.